Several to-dos

[zeehio]

These to-dos are leftovers from #13

To do things:

• Think of a better name for add_peaklist_rect. The syntax (plot(sample) + add_peaklist_rect(plot(sample),peaklist)) is weird. Can it be refactored to plot(sample) + geom_peaklist(peaklist) or since we also add a scale plot(sample)+overlay_peaklist(peaklist)?

• getChromatogram() and getSpectrum() should let us choose the aggregation function. So we can choose to either sum drifts (or retentions) or get the one with higher intensity in the range.

• getChromatogram() and getSpectrum() for GCIMSDataset objects. Maybe they have to return MChromatogram and MSpectrum objects, with a plot method? This could simplify smoothing and baseline plots in the vignette. These objects could also have a copy of pData(dataset) so the plot can use annotations. This would cover an implementation for getRIC(), getTIS(), plotRIC(), plotTIS() for GCIMSDataset objects.

• After realize() we should save the dataset object in the folder as well, so we can import the directory . An import function that takes such directory and changes the base_dir if it has been moved would be desirable.

• Add examples and documentation on how to add a realize action

Reading data

• Helpers for importing CSV files that are not overly specific to a software version
• Support nos/scm files

Physical units:

• Peak intensity in volts vs a.u.
• Support for reduced mobility units. Replace dt_range with ims_range and ims_unit ?
• Support for retention index units. rt_range -> gc_range & gc_unit ?
• find_rip verbosity information prints too many significant digits on drift time limits

Internal and external standards

• Conversion from Retention time to Retention index using additional samples (ketones mixture)
• Usage of internal standards (e.g. 4-fluorobenzaldehyde) for QC
• Plots showing the stability of the daily pools, if available

Plots

• plot(dataset, sample, dt_range, rt_range) (several samples in subplots, same intensity scale)
• align should save RIC and TIS before transforming samples, so we can get a before and after plot of them

Vignette and docs:

• Review vignette plots
• Each generic in its own help page, with a @family name-of-generic tag. Each method with the same family tag. This will make help pages easier to browse.
• Review docs from:
  • plot for GCIMSChromatogram and GCIMSSpectrum
  • tidy for GCIMSSample
  • add_peaklist_rect
  • create_annotations_table
  • getIMS, getChromatogram
  • integratePeaks
  • peaks
• Runnable examples for > 80% of functions of the new API